[English] 日本語
Yorodumi
- PDB-6jb9: Crystal structure of nanobody D3-L11 (unbound form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jb9
TitleCrystal structure of nanobody D3-L11 (unbound form)
ComponentsNanobody D3-L11
KeywordsIMMUNE SYSTEM / nanobody / hot-spot mutagenesis / thermodynamics / biomolecular recognition
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsCaaveiro, J.M.M. / Tamura, H. / Akiba, H. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K06962 Japan
Japan Society for the Promotion of Science16H02420 Japan
CitationJournal: Sci Rep / Year: 2019
Title: Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody.
Authors: Akiba, H. / Tamura, H. / Kiyoshi, M. / Yanaka, S. / Sugase, K. / Caaveiro, J.M.M. / Tsumoto, K.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nanobody D3-L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2665
Polymers13,8811
Non-polymers3844
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area6310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.190, 53.360, 36.210
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Nanobody D3-L11


Mass: 13881.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM TRIS HCl, 100mM NaCl, 2.0M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→26.7 Å / Num. obs: 34665 / % possible obs: 97.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 1.15→1.21 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6 / Num. unique obs: 4414 / CC1/2: 0.952 / % possible all: 85.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JB2

6jb2


Resolution: 1.15→26.69 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.85 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12903 643 1.9 %RANDOM
Rwork0.10159 ---
obs0.10211 33999 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.992 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.11 Å2
2--0.19 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.15→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 20 197 1191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131091
X-RAY DIFFRACTIONr_bond_other_d0.0010.018950
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.6441492
X-RAY DIFFRACTIONr_angle_other_deg1.6411.582214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4645147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36921.50953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07815175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.51157
X-RAY DIFFRACTIONr_chiral_restr0.1250.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02245
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0610.596546
X-RAY DIFFRACTIONr_mcbond_other1.0460.595545
X-RAY DIFFRACTIONr_mcangle_it1.3160.904686
X-RAY DIFFRACTIONr_mcangle_other1.3160.906687
X-RAY DIFFRACTIONr_scbond_it1.8920.823545
X-RAY DIFFRACTIONr_scbond_other1.5950.789528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8651.108775
X-RAY DIFFRACTIONr_long_range_B_refined2.8368.6971197
X-RAY DIFFRACTIONr_long_range_B_other2.5328.0461160
X-RAY DIFFRACTIONr_rigid_bond_restr4.0132041
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 36 -
Rwork0.153 1975 -
obs--77.76 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more